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###
### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data pgxRpi
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* checking for file ‘pgxRpi/DESCRIPTION’ ... OK
* preparing ‘pgxRpi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Introduction_1_load_metadata.Rmd’ using rmarkdown

Quitting from Introduction_1_load_metadata.Rmd:183-188 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (nrow(meta.sel.df) == 0) ...`:
! argument is of length zero
---
Backtrace:
    ▆
 1. └─pgxRpi::pgxMetaplot(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Introduction_1_load_metadata.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Introduction_1_load_metadata.Rmd’

--- re-building ‘Introduction_2_query_variants.Rmd’ using rmarkdown

Quitting from Introduction_2_query_variants.Rmd:76-79 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (grepl("^https?://", domain)) ...`:
! argument is of length zero
---
Backtrace:
    ▆
 1. └─pgxRpi::pgxLoader(type = "g_variants", biosample_id = biosample_id)
 2.   └─pgxRpi:::pgxVariantLoader(...)
 3.     └─pgxRpi:::read_variant_beacon(...)
 4.       └─pgxRpi:::normalize_domain(domain, use_https)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Introduction_2_query_variants.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Introduction_2_query_variants.Rmd’

--- re-building ‘Introduction_3_access_cnv_frequency.Rmd’ using rmarkdown

Quitting from Introduction_3_access_cnv_frequency.Rmd:49-54 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `pgxFreqLoader()`:
! Request failed for filter NCIT:C3058,NCIT:C3493 (status code: 422)
---
Backtrace:
    ▆
 1. └─pgxRpi::pgxLoader(...)
 2.   └─pgxRpi:::pgxFreqLoader(output = output, filters = filters, domain = domain)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Introduction_3_access_cnv_frequency.Rmd' failed with diagnostics:
Request failed for filter NCIT:C3058,NCIT:C3493 (status code: 422)
--- failed re-building ‘Introduction_3_access_cnv_frequency.Rmd’

--- re-building ‘Introduction_4_process_pgxseg.Rmd’ using rmarkdown
--- finished re-building ‘Introduction_4_process_pgxseg.Rmd’

SUMMARY: processing the following files failed:
  ‘Introduction_1_load_metadata.Rmd’
  ‘Introduction_2_query_variants.Rmd’
  ‘Introduction_3_access_cnv_frequency.Rmd’

Error: Vignette re-building failed.
Execution halted